PY6
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| N1 | C2 | doub | 1.32Å | 1.38Å | Aromatic |
| N1 | C6 | sing | 1.32Å | 1.36Å | Aromatic |
| C2 | C2A | sing | 1.51Å | 1.52Å | |
| C2 | C3 | sing | 1.39Å | 1.44Å | Aromatic |
| C2A | H2A1 | sing | 1.09Å | 1.11Å | |
| C2A | H2A2 | sing | 1.09Å | 1.11Å | |
| C2A | H2A3 | sing | 1.09Å | 1.12Å | |
| C3 | O3 | sing | 1.36Å | 1.35Å | |
| C3 | C4 | doub | 1.39Å | 1.41Å | Aromatic |
| O3 | HO3 | sing | 0.97Å | 0.95Å | |
| C4 | C4A | sing | 1.51Å | 1.52Å | |
| C4 | C5 | sing | 1.38Å | 1.44Å | Aromatic |
| C4A | N | sing | 1.47Å | 1.51Å | |
| C4A | H4A1 | sing | 1.09Å | 1.12Å | |
| C4A | H4A2 | sing | 1.09Å | 1.12Å | |
| C5 | C6 | doub | 1.38Å | 1.38Å | Aromatic |
| C5 | C5A | sing | 1.51Å | 1.53Å | |
| C6 | H6 | sing | 1.08Å | 1.10Å | |
| C5A | O4P | sing | 1.43Å | 1.38Å | |
| C5A | H5A1 | sing | 1.09Å | 1.12Å | |
| C5A | H5A2 | sing | 1.09Å | 1.12Å | |
| O4P | P | sing | 1.61Å | 1.59Å | |
| P | O1P | doub | 1.48Å | 1.43Å | |
| P | O2P | sing | 1.61Å | 1.50Å | |
| P | O3P | sing | 1.61Å | 1.49Å | |
| O2P | HOP2 | sing | 0.97Å | 0.95Å | |
| O3P | HOP3 | sing | 0.97Å | 0.95Å | |
| N | CA | sing | 1.47Å | 1.50Å | |
| N | HN2 | sing | 1.01Å | 1.02Å | |
| CA | C | sing | 1.51Å | 1.51Å | |
| CA | CB | sing | 1.53Å | 1.53Å | |
| CA | HA | sing | 1.09Å | 1.12Å | |
| C | O | doub | 1.21Å | 1.35Å | |
| C | OXT | sing | 1.34Å | 1.29Å | |
| CB | CG | sing | 1.53Å | 1.52Å | |
| CB | HB1 | sing | 1.09Å | 1.11Å | |
| CB | HB2 | sing | 1.09Å | 1.12Å | |
| CG | CD | sing | 1.53Å | 1.52Å | |
| CG | HG1 | sing | 1.09Å | 1.12Å | |
| CG | HG2 | sing | 1.09Å | 1.11Å | |
| CD | CE | sing | 1.53Å | 1.52Å | |
| CD | HD1 | sing | 1.09Å | 1.11Å | |
| CD | HD2 | sing | 1.09Å | 1.12Å | |
| CE | HE1 | sing | 1.09Å | 1.12Å | |
| CE | HE2 | sing | 1.09Å | 1.12Å | |
| CE | HE3 | sing | 1.09Å | 1.11Å | |
| OXT | HXT | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C2 | N1 | C6 | 122.3° | 121.8° |
| N1 | C2 | C2A | 109.5° | 119.7° |
| N1 | C2 | C3 | 117.9° | 120.7° |
| N1 | C6 | C5 | 118.0° | 120.9° |
| N1 | C6 | H6 | 120.4° | 119.6° |
| C2A | C2 | C3 | 132.5° | 119.6° |
| C2 | C2A | H2A1 | 109.5° | 109.5° |
| C2 | C2A | H2A2 | 112.1° | 109.5° |
| C2 | C2A | H2A3 | 112.1° | 109.5° |
| C2 | C3 | O3 | 110.9° | 120.5° |
| C2 | C3 | C4 | 123.6° | 119.0° |
| H2A1 | C2A | H2A2 | 112.2° | 109.4° |
| H2A1 | C2A | H2A3 | 112.2° | 109.5° |
| H2A2 | C2A | H2A3 | 98.3° | 109.4° |
| O3 | C3 | C4 | 125.5° | 120.5° |
| C3 | O3 | HO3 | 110.8° | 106.7° |
| C3 | C4 | C4A | 122.3° | 120.8° |
| C3 | C4 | C5 | 112.1° | 118.4° |
| C4A | C4 | C5 | 125.6° | 120.8° |
| C4 | C4A | N | 103.1° | 109.4° |
| C4 | C4A | H4A1 | 114.6° | 109.5° |
| C4 | C4A | H4A2 | 114.6° | 109.4° |
| C4 | C5 | C6 | 126.1° | 119.2° |
| C4 | C5 | C5A | 122.4° | 120.3° |
| N | C4A | H4A1 | 114.7° | 109.5° |
| N | C4A | H4A2 | 114.7° | 109.5° |
| C4A | N | CA | 110.6° | 106.7° |
| C4A | N | HN2 | 111.8° | 106.7° |
| H4A1 | C4A | H4A2 | 95.8° | 109.5° |
| C6 | C5 | C5A | 111.5° | 120.4° |
| C5 | C6 | H6 | 121.7° | 119.5° |
| C5 | C5A | O4P | 118.7° | 109.5° |
| C5 | C5A | H5A1 | 108.9° | 109.4° |
| C5 | C5A | H5A2 | 108.9° | 109.5° |
| O4P | C5A | H5A1 | 108.8° | 109.4° |
| O4P | C5A | H5A2 | 108.8° | 109.5° |
| C5A | O4P | P | 122.7° | 106.8° |
| H5A1 | C5A | H5A2 | 101.2° | 109.6° |
| O4P | P | O1P | 112.8° | 109.5° |
| O4P | P | O2P | 104.2° | 109.5° |
| O4P | P | O3P | 104.5° | 109.5° |
| O1P | P | O2P | 122.8° | 109.5° |
| O1P | P | O3P | 101.8° | 109.4° |
| O2P | P | O3P | 109.5° | 109.5° |
| P | O2P | HOP2 | 104.2° | 106.8° |
| P | O3P | HOP3 | 104.5° | 106.8° |
| CA | N | HN2 | 111.8° | 106.7° |
| N | CA | C | 108.4° | 109.4° |
| N | CA | CB | 111.1° | 109.5° |
| N | CA | HA | 109.8° | 109.5° |
| C | CA | CB | 111.4° | 109.5° |
| C | CA | HA | 109.4° | 109.5° |
| CA | C | O | 110.6° | 120.0° |
| CA | C | OXT | 124.6° | 120.1° |
| CB | CA | HA | 106.6° | 109.5° |
| CA | CB | CG | 115.2° | 109.5° |
| CA | CB | HB1 | 110.2° | 109.5° |
| CA | CB | HB2 | 110.1° | 109.4° |
| O | C | OXT | 124.8° | 120.0° |
| C | OXT | HXT | 124.6° | 120.0° |
| CG | CB | HB1 | 110.1° | 109.5° |
| CG | CB | HB2 | 110.1° | 109.5° |
| CB | CG | CD | 112.0° | 109.5° |
| CB | CG | HG1 | 111.3° | 109.4° |
| CB | CG | HG2 | 111.3° | 109.5° |
| HB1 | CB | HB2 | 100.1° | 109.4° |
| CD | CG | HG1 | 111.2° | 109.5° |
| CD | CG | HG2 | 111.3° | 109.5° |
| CG | CD | CE | 113.5° | 109.5° |
| CG | CD | HD1 | 110.8° | 109.5° |
| CG | CD | HD2 | 110.8° | 109.5° |
| HG1 | CG | HG2 | 99.1° | 109.4° |
| CE | CD | HD1 | 110.7° | 109.4° |
| CE | CD | HD2 | 110.7° | 109.4° |
| CD | CE | HE1 | 113.5° | 109.5° |
| CD | CE | HE2 | 110.8° | 109.5° |
| CD | CE | HE3 | 110.8° | 109.5° |
| HD1 | CD | HD2 | 99.5° | 109.5° |
| HE1 | CE | HE2 | 110.7° | 109.4° |
| HE1 | CE | HE3 | 110.8° | 109.4° |
| HE2 | CE | HE3 | 99.5° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| N1 | C2 | C2A | C3 | 179.5° | 180.0° |
| N1 | C2 | C2A | H2A1 | 180.0° | 90.0° |
| N1 | C2 | C2A | H2A2 | 54.7° | 30.0° |
| N1 | C2 | C2A | H2A3 | 54.8° | 150.0° |
| N1 | C2 | C3 | O3 | 179.9° | 180.0° |
| N1 | C2 | C3 | C4 | 0.5° | 0.0° |
| C2 | N1 | C6 | C5 | 0.4° | 0.2° |
| C2 | N1 | C6 | H6 | 179.6° | 180.0° |
| C6 | N1 | C2 | C2A | 179.9° | 180.0° |
| C6 | N1 | C2 | C3 | 0.5° | 0.0° |
| N1 | C6 | C5 | C4 | 0.3° | 0.5° |
| N1 | C6 | C5 | H6 | 180.0° | 179.8° |
| N1 | C6 | C5 | C5A | 179.9° | 180.0° |
| C2 | C2A | H2A1 | H2A2 | 125.2° | 120.0° |
| C2 | C2A | H2A1 | H2A3 | 125.2° | 120.1° |
| C2 | C2A | H2A2 | H2A3 | 118.0° | 120.0° |
| C2A | C2 | C3 | O3 | 0.6° | 0.0° |
| C2A | C2 | C3 | C4 | 180.0° | 180.0° |
| C3 | C2 | C2A | H2A1 | 0.5° | 90.1° |
| C3 | C2 | C2A | H2A2 | 124.8° | 150.0° |
| C3 | C2 | C2A | H2A3 | 125.7° | 30.0° |
| C2 | C3 | O3 | C4 | 179.5° | 180.0° |
| C2 | C3 | O3 | HO3 | 180.0° | 89.9° |
| C2 | C3 | C4 | C4A | 179.8° | 179.9° |
| C2 | C3 | C4 | C5 | 0.3° | 0.3° |
| H2A1 | C2A | H2A2 | H2A3 | 118.1° | 120.0° |
| O3 | C3 | C4 | C4A | 0.5° | 0.0° |
| O3 | C3 | C4 | C5 | 179.7° | 179.7° |
| C4 | C3 | O3 | HO3 | 0.5° | 90.0° |
| C3 | C4 | C4A | C5 | 179.8° | 179.7° |
| C3 | C4 | C4A | N | 28.4° | 90.0° |
| C3 | C4 | C4A | H4A1 | 96.9° | 29.9° |
| C3 | C4 | C4A | H4A2 | 153.7° | 150.0° |
| C3 | C4 | C5 | C6 | 0.3° | 0.5° |
| C3 | C4 | C5 | C5A | 179.8° | 180.0° |
| C4 | C4A | N | H4A1 | 125.3° | 119.9° |
| C4 | C4A | N | H4A2 | 125.3° | 120.0° |
| C4 | C4A | H4A1 | H4A2 | 120.4° | 120.0° |
| C4A | C4 | C5 | C6 | 179.9° | 179.8° |
| C4A | C4 | C5 | C5A | 0.4° | 0.3° |
| C4 | C4A | N | CA | 157.3° | 180.0° |
| C4 | C4A | N | HN2 | 32.0° | 66.2° |
| C5 | C4 | C4A | N | 151.4° | 90.3° |
| C5 | C4 | C4A | H4A1 | 83.3° | 149.8° |
| C5 | C4 | C4A | H4A2 | 26.1° | 29.7° |
| C4 | C5 | C6 | C5A | 179.6° | 179.5° |
| C4 | C5 | C6 | H6 | 179.7° | 179.7° |
| C4 | C5 | C5A | O4P | 20.7° | 179.5° |
| C4 | C5 | C5A | H5A1 | 145.9° | 60.6° |
| C4 | C5 | C5A | H5A2 | 104.6° | 59.5° |
| N | C4A | H4A1 | H4A2 | 120.5° | 120.1° |
| C4A | N | CA | HN2 | 125.2° | 113.8° |
| C4A | N | CA | C | 179.9° | 90.0° |
| C4A | N | CA | CB | 57.3° | 150.0° |
| C4A | N | CA | HA | 60.4° | 30.0° |
| H4A1 | C4A | N | CA | 32.0° | 60.0° |
| H4A1 | C4A | N | HN2 | 93.2° | 173.9° |
| H4A2 | C4A | N | CA | 77.5° | 60.1° |
| H4A2 | C4A | N | HN2 | 157.3° | 53.8° |
| C6 | C5 | C5A | O4P | 158.9° | 0.0° |
| C6 | C5 | C5A | H5A1 | 33.6° | 119.9° |
| C6 | C5 | C5A | H5A2 | 75.9° | 120.1° |
| C5A | C5 | C6 | H6 | 0.1° | 0.2° |
| C5 | C5A | O4P | H5A1 | 125.3° | 119.9° |
| C5 | C5A | O4P | H5A2 | 125.3° | 120.0° |
| C5 | C5A | H5A1 | H5A2 | 114.6° | 120.0° |
| C5 | C5A | O4P | P | 151.2° | 180.0° |
| O4P | C5A | H5A1 | H5A2 | 114.5° | 120.1° |
| C5A | O4P | P | O1P | 51.8° | 59.9° |
| C5A | O4P | P | O2P | 172.8° | 180.0° |
| C5A | O4P | P | O3P | 57.9° | 60.0° |
| H5A1 | C5A | O4P | P | 25.9° | 60.1° |
| H5A2 | C5A | O4P | P | 83.5° | 60.0° |
| O4P | P | O1P | O2P | 125.9° | 120.0° |
| O4P | P | O1P | O3P | 111.4° | 120.0° |
| O4P | P | O2P | O3P | 111.3° | 120.0° |
| O4P | P | O2P | HOP2 | 180.0° | 180.0° |
| O4P | P | O3P | HOP3 | 180.0° | 60.0° |
| O1P | P | O2P | O3P | 119.1° | 120.0° |
| O1P | P | O2P | HOP2 | 50.4° | 60.0° |
| O1P | P | O3P | HOP3 | 62.4° | 180.0° |
| O2P | P | O3P | HOP3 | 68.9° | 60.0° |
| O3P | P | O2P | HOP2 | 68.7° | 60.0° |
| N | CA | C | CB | 122.5° | 120.0° |
| N | CA | C | HA | 119.8° | 120.0° |
| N | CA | CB | HA | 119.6° | 120.0° |
| N | CA | C | O | 48.8° | 150.0° |
| N | CA | C | OXT | 131.0° | 30.0° |
| N | CA | CB | CG | 56.7° | 60.0° |
| N | CA | CB | HB1 | 178.0° | 179.9° |
| N | CA | CB | HB2 | 68.6° | 60.0° |
| HN2 | N | CA | C | 54.7° | 23.8° |
| HN2 | N | CA | CB | 177.4° | 96.2° |
| HN2 | N | CA | HA | 64.9° | 143.8° |
| C | CA | CB | HA | 119.4° | 120.0° |
| CA | C | O | OXT | 179.7° | 179.9° |
| C | CA | CB | CG | 64.3° | 180.0° |
| C | CA | CB | HB1 | 60.9° | 60.0° |
| C | CA | CB | HB2 | 170.4° | 59.9° |
| CA | C | OXT | HXT | 180.0° | 180.0° |
| CB | CA | C | O | 171.3° | 90.0° |
| CB | CA | C | OXT | 8.4° | 90.0° |
| CA | CB | CG | HB1 | 125.3° | 120.0° |
| CA | CB | CG | HB2 | 125.3° | 120.0° |
| CA | CB | HB1 | HB2 | 116.0° | 119.9° |
| CA | CB | CG | CD | 168.2° | 180.0° |
| CA | CB | CG | HG1 | 43.0° | 60.0° |
| CA | CB | CG | HG2 | 66.6° | 60.0° |
| HA | CA | C | O | 71.0° | 30.0° |
| HA | CA | C | OXT | 109.3° | 150.0° |
| HA | CA | CB | CG | 176.3° | 60.0° |
| HA | CA | CB | HB1 | 58.4° | 60.1° |
| HA | CA | CB | HB2 | 51.0° | 179.9° |
| O | C | OXT | HXT | 0.3° | 0.1° |
| CG | CB | HB1 | HB2 | 115.9° | 120.0° |
| CB | CG | CD | HG1 | 125.2° | 120.0° |
| CB | CG | CD | HG2 | 125.3° | 120.1° |
| CB | CG | HG1 | HG2 | 117.2° | 120.0° |
| CB | CG | CD | CE | 79.9° | 180.0° |
| CB | CG | CD | HD1 | 154.8° | 60.1° |
| CB | CG | CD | HD2 | 45.3° | 60.0° |
| HB1 | CB | CG | CD | 66.5° | 60.0° |
| HB1 | CB | CG | HG1 | 168.3° | 180.0° |
| HB1 | CB | CG | HG2 | 58.7° | 60.1° |
| HB2 | CB | CG | CD | 42.9° | 60.0° |
| HB2 | CB | CG | HG1 | 82.3° | 60.0° |
| HB2 | CB | CG | HG2 | 168.2° | 180.0° |
| CD | CG | HG1 | HG2 | 117.2° | 120.0° |
| CG | CD | CE | HD1 | 125.3° | 120.0° |
| CG | CD | CE | HD2 | 125.2° | 120.0° |
| CG | CD | HD1 | HD2 | 116.6° | 120.1° |
| CG | CD | CE | HE1 | 180.0° | 180.0° |
| CG | CD | CE | HE2 | 54.7° | 60.0° |
| CG | CD | CE | HE3 | 54.7° | 60.0° |
| HG1 | CG | CD | CE | 45.3° | 60.0° |
| HG1 | CG | CD | HD1 | 80.0° | 180.0° |
| HG1 | CG | CD | HD2 | 170.5° | 60.0° |
| HG2 | CG | CD | CE | 154.8° | 60.0° |
| HG2 | CG | CD | HD1 | 29.5° | 60.0° |
| HG2 | CG | CD | HD2 | 79.9° | 179.9° |
| CE | CD | HD1 | HD2 | 116.6° | 120.0° |
| CD | CE | HE1 | HE2 | 125.3° | 120.0° |
| CD | CE | HE1 | HE3 | 125.3° | 120.0° |
| CD | CE | HE2 | HE3 | 116.6° | 120.1° |
| HD1 | CD | CE | HE1 | 54.7° | 60.0° |
| HD1 | CD | CE | HE2 | 179.9° | 59.9° |
| HD1 | CD | CE | HE3 | 70.6° | 180.0° |
| HD2 | CD | CE | HE1 | 54.7° | 60.0° |
| HD2 | CD | CE | HE2 | 70.5° | 179.9° |
| HD2 | CD | CE | HE3 | 180.0° | 60.0° |
| HE1 | CE | HE2 | HE3 | 116.6° | 119.9° |
